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Crystal structure of the ectodomain of bovine viral diarrhea virus 1 E2 envelope protein
Analyse Crystal structure of the ectodomain of bovine viral diarrhea virus 1 E2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JNT
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein E2
- UniProt
- P19711
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Envelope glycoprotein E2 | protein | 324 | 1% helix, 47% strand | P19711 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.70 | 0.97 | 16 | empty |
| 2 | 74 | 0.56 | 0.86 | 21 | empty |
| 3 | 59 | 0.49 | 0.85 | 21 | empty |
| 4 | 99 | 0.44 | 0.78 | 14 | empty |
| 5 | 81 | 0.36 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 517 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4JNT · Crystal structure of the ectodomain of Bovine viral diarrhea virus 1 E2 envelope protein · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P19711
- Elsewhere: RCSB PDB 4JNT · PDBe 4JNT · UniProt P19711
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